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Data Mining in Ensembl with Data Mining in Ensembl with BioMartBioMart

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Simple Text-based Simple Text-based Search EngineSearch Engine

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‘‘Mouse Gene’ Gives Us ResultsMouse Gene’ Gives Us Results

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A More Complex Query is Not as A More Complex Query is Not as UsefulUseful

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BioMart- Data miningBioMart- Data mining• BioMart is a search engine that can

find multiple terms and put them into a table format.

• Such as: human gene (IDs), chromosome and base pair position

• No programming required!

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General or Specific Data-TablesGeneral or Specific Data-Tables

• All the genes for one species

• Or… only genes on one specific region of a chromosome

• Or… genes on one region of a chromosome associated with a disease

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BioMart Data SetsBioMart Data Sets• Ensembl genes• Vega genes• SNPs

• Markers• Phenotypes• Gene expression information• Gene ontology• Homology predictions• Protein annotation

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Web InterfaceWeb Interface

With BioMart, quickly extract gene-associated information from the Ensembl databases.

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Information FlowInformation Flow• Choose the species of interest (Dataset)

• Decide what you would like to know about the genes (Attributes)(sequences, IDs, description…)

• Decide on a smaller geneset using Filters.(enter IDs, choose a region …)

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Web InterfaceWeb Interface

Three main stages: Dataset, Attributes and Filters.

Choose the species of

interest

Choose what information

to view.

Choose the gene set using what we know.

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The First Step: Choose the DatasetThe First Step: Choose the Dataset

Homo sapiensgenes are the

default.

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The Second Step: AttributesThe Second Step: Attributes

Attributes are what we want to know about the genes.

Four output pages.

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TheThe SNP Attribute PageSNP Attribute Page

Output variation information such as SNP reference ID and alleles.

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Filters Allow Gene SelectionFilters Allow Gene Selection

Choose the gene set by region, gene ID(s), protein/domain type.

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Export Sequence or TablesExport Sequence or Tables

Genes and attributes are exported as sequence (Fasta format) or tables.

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Query:Query:

• For all mouse genes on chromosome 10 that are protein coding, I would like to know the IDs in both Ensembl and MGI.

• In the query:Attributes: what we want to know.Filters: what we know

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Query:Query:

• For all mouse genes on chromosome 10 that are protein coding, I would like to know the IDs in both Ensembl and MGI.

• In the query:Attributes: what we want to know.Filters: what we know

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Query:Query:

• For all mouse genes on chromosome 10 that are protein coding, I would like to know the IDs in both Ensembl and MGI.

• In the query:Attributes: what we want to know.Filters: what we know

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A Brief ExampleA Brief ExampleChange dataset to

mouseMus musculus

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A Brief ExampleA Brief Example

Dataset has changed.

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Attributes (Output Options)Attributes (Output Options)

ClickAttributes.

Attributes allow us to choose what we wish to know.

IDs are found in the ‘Features’ page.

Click on ‘GENE’.

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Default options selected:Ensembl Gene ID and Transcript ID

Attributes (Output Options)Attributes (Output Options)

Ensembl Gene ID is selected

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Scroll down to select MGI symbol.Also select the accession number.

Attributes (Output Options)Attributes (Output Options)

‘Markersymbol ID’ will give us the MGI ID

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‘Results’ give us Gene IDs for all mouse genes in the Ensembl database.

The Results TableThe Results Table

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Select a Smaller Gene SetSelect a Smaller Gene Set

Select ‘Filters’

Expand the REGION panel

Instead of all mouse genes, select protein coding genes on chromosome 10.

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Select Genes on Chromosome 10Select Genes on Chromosome 10

Select chromosome

10

Instead of all mouse genes, select protein coding genes on chromosome 10.

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Select Protein Coding GenesSelect Protein Coding Genes

Filters are set to chromosome 10 and protein-coding genes. Genes must meet BOTH

criteria to be in the result table.

Gene type:protein coding

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Results (Preview)Results (Preview)

This is a preview- if you are happy with the table, click ‘Go’.

For the full result table: Go

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Full Result TableFull Result Table

Ensembl Gene IDTranscript

IDMGI

symbolMGI Accession

Number

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Original Query:Original Query:

• For all mouse genes on chromosome 10 that are protein coding, I would like to know the IDs in both Ensembl and MGI.

• In the query:Attributes: columns in the Result TableFilters: what we know

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Other Export Options (Attributes)Other Export Options (Attributes)• Sequences: UTRs, flanking sequences, cDNA

and peptides, etc

• Gene IDs from Ensembl and external sources (MGI, Entrez, etc.)

• Microarray data

• Protein Functions/descriptions (Interpro, GO)

• Orthologous gene sets

• SNP/ Variation Data

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Central ServerCentral Server

www.biomart.org

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WormBase WormBase

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HapMapHapMap

Population frequencies

Inter- population comparisons

Gene annotation

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DictyBaseDictyBase

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Uniprot, MSDUniprot, MSD

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GRAMENEGRAMENE

Rice, Maize, Arabidopsis genomes…

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How to Get ThereHow to Get There

• Either www.biomart.org/biomart/martview

• Or click on ‘BioMart’ from Ensembl

QQ&&AAThanks Arek Kasprzyk

Benoît BallesterSyed HaiderRichard HollandDamian Smedley